I think Isaac is talking about the search input in layout.master which is on every page unless configured for link only and Crispin is talking about the /SearchResults.aspx page search input.
I will fix the Searchresults.aspx page so it focuses the search input by default. But I agree with Isaac that when the actual search box is shown on every page via layout.master it should not default to focused there, though if someone prefers that they can achieve it using the solution Isaac mentioned.
Best,
Joe